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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Tagged Files for CombineVariants in Queue?
The 3.2 CombineVariants Queue extension does not seem to pass through the TaggedFile information. I assume the extension generator is not recognizing the particular input type used by CombineVariants…
this.V = List(new TaggedFile("file1.vcf","file1"), new TaggedFile("file2.vcf","file2"))
in a Scala class that extends CombineVariants will produce:
-V file1.vcf -V file2.vcf
without the tags.